|
| Status |
Public on Oct 31, 2018 |
| Title |
HFD_0h_LPS_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal macrophages
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Peritoneal macrophages
diet: high fat
lps_treatment: 0h
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted uisng the Qiagen RNAeasy mini kit
Libraries were constructed using the NuGen Ovation Universal RNA-seq kit
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FH_0h_7_S17_R1_001
|
| Data processing |
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of read counts per gene
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Menno de Winther |
| E-mail(s) |
m.dewinther@amc.uva.nl
|
| Phone |
+31205666762
|
| Organization name |
Academic Medical Center University of Amsterdam
|
| Department |
Medical Biochemistry
|
| Lab |
Experimental Vascular Biology
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE107412 |
A defective pentose phosphate pathway reduces inflammatory macrophage responses during hypercholesterolemia |
|
| Relations |
| BioSample |
SAMN08103882 |
| SRA |
SRX3425818 |
